Stable carbon isotope analysis of nucleic acids to trace sources of dissolved substrates used by estuarine bacteria

Microbial inputs at the litter layer translate climate into altered organic matter properties

Plant litter chemistry is altered during decomposition but it remains unknown if these alterations, and thus the composition of residual litter, will change in response to climate. Selective microbial mineralization of litter components and the accumulation of microbial necromass can drive litter compositional change, but the extent to which these mechanisms respond to climate remains poorly understood. We addressed this knowledge gap by studying needle litter decomposition along a boreal forest climate transect. Specifically, we investigated how the composition and/or metabolism of the decomposer community varies with climate, and if that variation is associated with distinct modifications of litter chemistry during decomposition. We analyzed the composition of microbial phospholipid fatty acids (PLFAs) in the litter layer and measured natural abundance δ¹³ C_PLFA values as an integrated measure of microbial metabolisms. Changes in litter chemistry and δ¹³ C values were measured in litterbag experiments conducted at each transect site. A warmer climate was associated with higher litter nitrogen concentrations as well as altered microbial community structure (lower fungi:bacteria ratios) and microbial metabolism (higher δ¹³ C_PLFA ). Litter in warmer transect regions accumulated less aliphatic-C (lipids, waxes) and retained more O-alkyl-C (carbohydrates), consistent with enhanced ¹³ C-enrichment in residual litter, than in colder regions. These results suggest that chemical changes during litter decomposition will change with climate, driven primarily by indirect climate effects (e.g., greater nitrogen availability and decreased fungi:bacteria ratios) rather than direct temperature effects. A positive correlation between microbial biomass δ¹³ C values and ¹³ C-enrichment during decomposition suggests that change in litter chemistry is driven more by distinct microbial necromass inputs than differences in the selective removal of litter components. Our study highlights the role that microbial inputs during early litter decomposition can play in shaping surface litter contribution to soil organic matter as it responds to climate warming effects such as greater nitrogen availability.

Trophic importance of microphytobenthos and bacteria to meiofauna in soft-bottom intertidal habitats: A combined trophic marker approach

Meiofauna can play an important role in the carbon fluxes of soft-bottom coastal habitats. Investigation of their feeding behavior and trophic position remains challenging due to their small size. In this study, we determine and compare the food sources used by nematodes and benthic copepods by using stable isotope compositions, fatty acid profiles and compound specific isotope analyses of fatty acids in the mudflats, seagrass beds and a sandflat of the Marennes-Oléron Bay, France, and the Sylt-Rømø Bight, Germany. Suspended particulate organic matter was much more ¹³C-depleted than other food sources and meiofauna, highlighting its poor role in the different studied habitats. The very low proportions of vascular plant fatty acid markers in meiofauna demonstrated that these consumers did not rely on this food source, either fresh or detrital, even in seagrass beds. The combined use of stable isotopes and fatty acids emphasized microphytobenthos and benthic bacteria as the major food sources of nematodes and benthic copepods. Compound specific analyses of a bacteria marker confirmed that bacteria mostly used microphytobenthos as a substrate.

Tracing the role of endogenous carbon in denitrification using wine industry by-product as an external electron donor: Coupling isotopic tools with mathematical modeling

Nitrate removal through enhanced biological denitrification (EBD), consisting of the inoculation of an external electron donor, is a feasible solution for the recovery of groundwater quality. In this context, liquid waste from wine industries (wine industry by-products, WIB) may be feasible for use as a reactant to enhance heterotrophic denitrification. To address the feasibility of WIB as electron donor to promote denitrification, as well as to evaluate the role of biomass as a secondary organic C source, a flow-through experiment was carried out. Chemical and isotopic characterization was performed and coupled with mathematical modeling. Complete nitrate attenuation with no nitrite accumulation was successfully achieved after 10 days. Four different C/N molar ratios (7.0, 2.0, 1.0 and 0) were tested. Progressive decrease of the C/N ratio reduced the remaining C in the outflow and favored biomass migration, producing significant changes in dispersivity in the reactor, which favored efficient nitrate degradation. The applied mathematical model described the general trends for nitrate, ethanol, dissolved organic carbon (DOC) and dissolved inorganic carbon (DIC) concentrations. This model shows how the biomass present in the system is degraded to dissolved organic C (DOC_en) and becomes the main source of DOC for a C/N ratio between 1.0 and 0. The isotopic model developed for organic and inorganic carbon also describes the general trends of δ¹³C of ethanol, DOC and DIC in the outflow water. The study of the evolution of the isotopic fractionation of organic C using a Rayleigh distillation model shows the shift in the organic carbon source from the WIB to the biomass and is in agreement with the isotopic fractionation values used to calibrate the model. Isotopic fractionations (ε) of C-ethanol and C-DOC_en were -1‰ and -5‰ (model) and -3.3‰ and -4.8‰ (Rayleigh), respectively. In addition, an inverse isotopic fractionation of +10‰ was observed for biomass degradation to DOC_en. Overall, WIB can efficiently promote nitrate reduction in EBD treatments. The conceptual model of the organic C cycle and the developed mathematical model accurately described the chemical and isotopic transformations that occur during this induced denitrification.

Sequential bioavailability of sedimentary organic matter to heterotrophic bacteria

Aquatic sediments harbour diverse microbial communities that mediate organic matter degradation and influence biogeochemical cycles. The pool of bioavailable carbon continuously changes as a result of abiotic processes and microbial activity. It remains unclear how microbial communities respond to heterogeneous organic matrices and how this ultimately affects heterotrophic respiration. To explore the relationships between the degradation of mixed carbon substrates and microbial activity, we incubated batches of organic-rich sediments in a novel bioreactor (IsoCaRB) that permitted continuous observations of CO₂ production rates, as well as sequential sampling of isotopic signatures (δ¹³ C, Δ¹⁴ C), microbial community structure and diversity, and extracellular enzyme activity. Our results indicated that lower molecular weight (MW), labile, phytoplankton-derived compounds were degraded first, followed by petroleum-derived exogenous pollutants, and finally by higher MW polymeric plant material. This shift in utilization coincided with a community succession and increased extracellular enzyme activities. Thus, sequential utilization of different carbon pools induced changes at both the community and cellular level, shifting community composition, enzyme activity, respiration rates, and residual organic matter reactivity. Our results provide novel insight into the accessibility of sedimentary organic matter and demonstrate how bioavailability of natural organic substrates may affect the function and composition of heterotrophic bacterial populations.

Sources, Ages, and Alteration of Organic Matter in Estuaries

Understanding the processes influencing the sources and fate of organic matter (OM) in estuaries is important for quantifying the contributions of carbon from land and rivers to the global carbon budget of the coastal ocean. Estuaries are sites of high OM production and processing, and understanding biogeochemical processes within these regions is key to quantifying organic carbon (Corg) budgets at the land-ocean margin. These regions provide vital ecological services, including nutrient filtration and protection from floods and storm surge, and provide habitat and nursery areas for numerous commercially important species. Human activities have modified estuarine systems over time, resulting in changes in the production, respiration, burial, and export of Corg. Corg in estuaries is derived from aquatic, terrigenous, and anthropogenic sources, with each source exhibiting a spectrum of ages and lability. The complex source and age characteristics of Corg in estuaries complicate our ability to trace OM along the river-estuary-coastal ocean continuum. This review focuses on the application of organic biomarkers and compound-specific isotope analyses to estuarine environments and on how these tools have enhanced our ability to discern natural sources of OM, trace their incorporation into food webs, and enhance understanding of the fate of Corg within estuaries and their adjacent waters.

Strong influence of the littoral zone on sedimentary lipid biomarkers in a meromictic lake

Planktonic sulfur bacteria growing in zones of photic zone euxinia (PZE) are important primary producers in stratified, sulfur-rich environments. The potential for export and burial of microbial biomass from anoxic photic zones remains relatively understudied, despite being of fundamental importance to interpreting the geologic record of bulk total organic carbon (TOC) and individual lipid biomarkers. Here we report the relative concentrations and carbon isotope ratios of lipid biomarkers from the water column and sediments of meromictic Mahoney Lake. The data show that organic matter in the central basin sediments is indistinguishable from material at the lake shoreline in both its lipid and carbon isotopic compositions. However, this material is not consistent with either the lipid profile or carbon isotope composition of biomass obtained directly from the region of PZE. Due to the strong density stratification and the intensive carbon and sulfur recycling pathways in the water column, there appears to be minimal direct export of the sulfur-oxidizing planktonic community to depth. The results instead suggest that basinal sediments are sourced via the littoral environment, a system that integrates an indigenous shoreline microbial community, the degraded remains of laterally rafted biomass from the PZE community, and detrital remains of terrigenous higher plants. Material from the lake margins appears to travel downslope, traverse the strong density gradient, and become deposited in the deep basin; its final composition may be largely heterotrophic in origin. This suggests an important role for clastic and/or authigenic minerals in aiding the burial of terrigenous and mat-derived organic matter in euxinic systems. Downslope or mineral-aided transport of anoxygenic, photoautotrophic microbial mats may have been a significant sedimentation process in early Earth history.

A versatile method for simultaneous stable carbon isotope analysis of DNA and RNA nucleotides by liquid chromatography/isotope ratio mass spectrometry

RATIONALE

Liquid chromatography/isotope ratio mass spectrometry (LC/IRMS) is currently the most accurate and precise technique for the measurement of compound-specific stable carbon isotope ratios ((13)C/(12)C) in biological metabolites, at their natural abundance. However, until now this technique could not be applied for the analysis of nucleic acids, the building blocks of the carriers of genetic information in living cells and viruses, DNA and RNA.

METHODS

Mixed-mode chromatography (MMC) was applied to obtain the complete separation of nine nucleotides (eight originating from DNA/RNA and one nucleotide (inosine monophosphate) that may serve as an internal standard) in a single run using LC/IRMS. We also developed and validated a method for DNA and RNA extraction and an enzymatic hydrolysis protocol for natural samples, which is compatible with LC/IRMS analysis as it minimizes the carbon blank. The method was used to measure the concentration and stable carbon isotope ratio of DNA and RNA nucleotides in marine sediment and in the common marine macro alga (Ulva sp.) at natural abundance levels as well as for (13)C-enriched samples.

RESULTS

The detection limit of the LC/IRMS method varied between 1.0 nmol for most nucleotides and 2.0 nmol for late-eluting compounds. The intraday and interday reproducibility of nucleotide concentration measurements was better than, respectively, 4.1% and 8.9% and for δ(13)C measurements better than, respectively, 0.3‰ and 0.5‰. The obtained nucleic acid concentrations and nucleic acid synthesis rates were in good agreement with values reported in the literature.

CONCLUSIONS

This new method gives reproducible results for the concentration and δ(13)C values of nine nucleotides. This solvent-free chromatographic method may also be used for other purposes, such as for instance to determine nucleotide concentrations using spectrophotometric detection. This sensitive method offers a new avenue for the study of DNA and RNA biosynthesis that can be applied in various fields of research.

Lignocellulose-responsive bacteria in a southern California salt marsh identified by stable isotope probing

Carbon cycling by microbes has been recognized as the main mechanism of organic matter decomposition and export in coastal wetlands, yet very little is known about the functional diversity of specific groups of decomposers (e.g., bacteria) in salt marsh benthic trophic structure. Indeed, salt marsh sediment bacteria remain largely in a black box in terms of their diversity and functional roles within salt marsh benthic food web pathways. We used DNA stable isotope probing (SIP) utilizing ¹³C-labeled lignocellulose as a proxy to evaluate the fate of macrophyte-derived carbon in benthic salt marsh bacterial communities. Overall, 146 bacterial species were detected using SIP, of which only 12 lineages were shared between enriched and non-enriched communities. Abundant groups from the ¹³C-labeled community included Desulfosarcina, Spirochaeta, and Kangiella. This study is the first to use heavy-labeled lignocellulose to identify bacteria responsible for macrophyte carbon utilization in salt marsh sediments and will allow future studies to target specific lineages to elucidate their role in salt marsh carbon cycling and ultimately aid our understanding of the potential of salt marshes to store carbon.

Bacterial abundance and composition in marine sediments beneath the Ross Ice Shelf, Antarctica

Marine sediments of the Ross Sea, Antarctica, harbor microbial communities that play a significant role in the decomposition, mineralization, and recycling of organic carbon (OC). In this study, the cell densities within a 153-cm sediment core from the Ross Sea were estimated based on microbial phospholipid fatty acid (PLFA) concentrations and acridine orange direct cell counts. The resulting densities were as high as 1.7 × 10⁷ cells mL⁻¹ in the top ten centimeters of sediments. These densities are lower than those calculated for most near-shore sites but consistent with deep-sea locations with comparable sedimentation rates. The δ¹³C measurements of PLFAs and sedimentary and dissolved carbon sources, in combination with ribosomal RNA (SSU rRNA) gene pyrosequencing, were used to infer microbial metabolic pathways. The δ¹³C values of dissolved inorganic carbon (DIC) in porewaters ranged downcore from -2.5‰ to -3.7‰, while δ¹³C values for the corresponding sedimentary particulate OC (POC) varied from -26.2‰ to -23.1‰. The δ¹³C values of PLFAs ranged between -29‰ and -35‰ throughout the sediment core, consistent with a microbial community dominated by heterotrophs. The SSU rRNA gene pyrosequencing revealed that members of this microbial community were dominated by β-, δ-, and γ-Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Among the sequenced organisms, many appear to be related to known heterotrophs that utilize OC sources such as amino acids, oligosaccharides, and lactose, consistent with our interpretation from δ¹³CPLFA analysis. Integrating phospholipids analyses with porewater chemistry, δ¹³CDIC and δ¹³CPOC values and SSU rRNA gene sequences provides a more comprehensive understanding of microbial communities and carbon cycling in marine sediments, including those of this unique ice shelf environment.

Mammalian DNA δ15N exhibits 40‰ intramolecular variation and is unresponsive to dietary protein level

We report the first high-precision characterization of molecular and intramolecular δ(15)N of nucleosides derived from mammalian DNA. The influence of dietary protein level on brain amino acids and deoxyribonucleosides was determined to investigate whether high protein turnover would alter amino acid (15)N or (13)C values. Pregnant guinea pig dams were fed control diets, or high or low levels of dietary protein throughout gestation, and all pups were fed control diets. The cerebellar DNA of offspring was extracted at 2 and 120 days of life, nucleosides isolated and δ(15)N and δ(13)C values characterized. Mean diet δ(15)N was 0.45 ± 0.33‰, compared with cerebellar whole tissue and DNA δ(15) N= +4.1 ± 0.7‰ and -4.5 ± 0.4‰, respectively. Cerebellar deoxythymidine (dT), deoxycytidine (dC), deoxyadenosine (dA), and deoxyguanosine (dG) δ(15)N were +1.4 ± 0.4, -2.1 ± 0.9, -7.2 ± 0.3, and -10.4 ± 0.5‰, respectively. There were no changes in amino acid or deoxyribonucleoside δ(15) N values due to dietary protein level. Using known metabolic relationships, we developed equations to calculate the intramolecular δ(15)N values originating from aspartate (asp) in purines (pur) or pyrimidines (pyr), glutamine (glu), and glycine (gly) to be δ(15)N(ASP-PUR), δ(15)N(ASP-PYR), δ(15) N(GLN), and δ(15) N(GLY) +11.9 ± 2.3‰, +7.0 ± 2.0‰, -9.1 ± 2.4‰, and -31.8 ± 8.9‰, respectively. A subset of twelve amino acids from food and brain had mean δ(15) N values of 4.3 ± 3.2‰ and 13.8 ± 3.1‰, respectively, and δ(15)N values for gly and asp were 12.6 ± 2.2‰ and 15.2 ± 0.8‰, respectively. A separate isotope tracer study detected no significant turnover of cerebellar DNA in the first six months of life. The large negative δ(15)N difference between gly and cerebellar purine N at the gly (7) position implies either that there is a major isotope effect during DNA synthesis, or that in utero gly has a different isotope ratio during rapid growth and metabolism from that in adult life. Our data show that cerebellar nucleoside intramolecular δ(15)N values vary over more than 40‰ and are not influenced by dietary protein level or age.

Utilization of dissolved nitrogen by heterotrophic bacterioplankton: a comparison of three ecosystems

The contributions of different organic and inorganic nitrogen and organic carbon sources to heterotrophic bacterioplankton in batch cultures of oceanic, estuarine, and eutrophic riverine environments were compared. The importance of the studied compounds was surprisingly similar among the three ecosystems. Dissolved combined amino acids (DCAA) were most significant, sustaining from 10 to 45% of the bacterial carbon demands and from 42 to 112% of the bacterial nitrogen demands. Dissolved free amino acids (DFAA) supplied 2 to 7% of the carbon and 6 to 24% of the nitrogen incorporated into the bacterial biomass, while dissolved DNA (D-DNA) sustained less than 5 and 12% of the carbon and nitrogen requirements, respectively. Ammonium was the second most important source of nitrogen, meeting from 13 to 45% of the bacterial demand in the oceanic and estuarine cultures and up to 270% of the demand in riverine cultures. Nitrate was taken up in the oceanic cultures (uptake equaled up to 46% of the nitrogen demand) but was released in the two others. Assimilation of DCAA, DFAA, and D-DNA combined supplied 43% of the carbon demand of the bacteria in the oceanic cultures, while approximately 25% of the carbon requirements were met by the three substrates at the two other sites. Assimilation of nitrogen from DCAA, DFAA, D-DNA, NH(4), and NO(3), on the other hand, exceeded production of particulate organic nitrogen in one culture at 27 h and in all cultures over the entire incubation period (50 h). These results suggest that the studied nutrient sources may fully support the nitrogen needs but only partially support the carbon needs of microbial communities of geographically different ecosystems. Furthermore, a comparison of the initial concentrations of the different substrates indicated that relative pool sizes of the substrates seemed to influence which substrates were primarily being utilized by the bacteria.

Linking microbial community function to phylogeny of sulfate-reducing Deltaproteobacteria in marine sediments by combining stable isotope probing with magnetic-bead capture hybridization of 16S rRNA

We further developed the stable isotope probing, magnetic-bead capture method to make it applicable for linking microbial community function to phylogeny at the class and family levels. The main improvements were a substantial decrease in the protocol blank and an approximately 10-fold increase in the detection limit by using a micro-elemental analyzer coupled to isotope ratio mass spectrometry to determine (13)C labeling of isolated 16S rRNA. We demonstrated the method by studying substrate utilization by Desulfobacteraceae, a dominant group of complete oxidizing sulfate-reducing Deltaproteobacteria in marine sediments. Stable-isotope-labeled [(13)C]glucose, [(13)C]propionate, or [(13)C]acetate was fed into an anoxic intertidal sediment. We applied a nested set of three biotin-labeled oligonucleotide probes to capture Bacteria, Deltaproteobacteria, and finally Desulfobacteraceae rRNA by using hydrophobic streptavidin-coated paramagnetic beads. The target specificities of the probes were examined with pure cultures of target and nontarget species and by determining the phylogenetic composition of the captured sediment rRNA. The specificity of the final protocol was generally very good, as more than 90% of the captured 16S rRNA belonged to the target range of the probes. Our results indicated that Desulfobacteraceae were important consumers of propionate but not of glucose. However, the results for acetate utilization were less conclusive due to lower and more variable labeling levels in captured rRNA. The main advantage of the method in this study over other nucleic acid-based stable isotope probing methods is that (13)C labeling can be much lower, to the extent that delta(13)C ratios can be studied even at their natural abundances.

The radiocarbon signature of microorganisms in the mesopelagic ocean

Several lines of evidence indicate that microorganisms in the meso- and bathypelagic ocean are metabolically active and respiring carbon. In addition, growing evidence suggests that archaea are fixing inorganic carbon in this environment. However, direct quantification of the contribution from deep ocean carbon sources to community production in the dark ocean remains a challenge. In this study, carbon flow through the microbial community at 2 depths in the mesopelagic zone of the North Pacific Subtropical Gyre was examined by exploiting the unique radiocarbon signatures (Delta(14)C) of the 3 major carbon sources in this environment. The radiocarbon content of nucleic acids, a biomarker for viable cells, isolated from size-fractionated particles (0.2-0.5 microm and >0.5 microm) showed the direct incorporation of carbon delivered by rapidly sinking particles. Most significantly, at the 2 mesopelagic depths examined (670 m and 915 m), carbon derived from in situ autotrophic fixation supported a significant fraction of the free-living microbial community (0.2-0.5 microm size fraction), but the contribution of chemoautotrophy varied markedly between the 2 depths. Results further showed that utilization of the ocean's largest reduced carbon reservoir, (14)C-depleted, dissolved organic carbon, was negligible in this environment. This isotopic portrait of carbon assimilation by the in situ, free-living microbial community, integrated over >50,000 L of seawater, implies that recent, photosynthetic carbon is not always the major carbon source supporting microbial community production in the mesopelagic realm.

Determination of the carbon isotopic composition of whole/intact biological specimens using at-line direct thermal desorption to effect thermally assisted hydrolysis/methylation

In this paper, we discuss the use of a direct thermal desorption (DTD) interface as an alternative to Curie-point flash pyrolysis system as an inlet technique in gas chromatography-combustion isotope-ratio mass spectrometry (GC/C-IRMS) analysis of whole/intact phytoplankton and zooplankton specimens. The DTD in combination with a combipal auto-injector is programmed to perform the injection, evaporation of solvents, transport of capped programmed-temperature vaporizer (PTV) liners to the PTV injector and chemical derivatisation (thermally assisted hydrolysis/methylation; THM) such that a profile of a cellular fatty acids is obtained. Flow-cytometric sorted microalgae and handpicked zooplankton are used as samples with trimethylsulfonium hydroxide (TMSH) as methylating reagent. A major advantage of this novel approach over the Curie-point technique is the automation of the total procedure, which allows unattended analysis of large sample series. The profiles and delta(13)C carbon isotopic signatures of the fatty acid methyl esters (FAMEs) produced are very similar to those obtained using the Curie-point flash pyrolysis method. It is shown that algal samples must be kept no longer than 48 h in the DTD sample tray prior to the THM-analysis in order to maintain the integrity of their FAME profile.

Differences of heterotrophic 13CO2 assimilation by Pseudomonas knackmussii strain B13 and Rhodococcus opacus 1CP and potential impact on biomarker stable isotope probing

Motivated by the finding that Pseudomonas knackmussii B13 but not Rhodococcus opacus 1CP grows in the absence of externally provided CO(2), we investigated the assimilation of (13)CO(2) into active cells cultivated with non-labelled glucose as sole energy substrate. (13)C found in the bulk biomass indicated a substantial but different CO(2) assimilation by Pseudomonas and Rhodococcus, respectively (3500 per thousand and 2600 per thousand). Cellular fatty acids were labelled from -15 per thousand to 470 per thousand and amino acids from 500 per thousand to 24,000 per thousand demonstrating clear differences between various compound classes. 'You are what you eat plus 1 per thousand' is therefore only valid for the average bulk C without specific isotope signature deviation of the external CO(2) or carbonates. Odd-numbered and 10-methyl fatty acids, which are much more abundant in Rhodococcus or other Gram-positive bacteria, were up to fivefold higher enriched in (13)C relative to the Pseudomonas fatty acids. A high-level growth-phase-independent, labelling of the oxaloacetate-derived amino acids indicated heterotrophic CO(2) fixation by anaplerotic reactions known to replenish the tricarboxylic acid cycle. Although both strains assimilate CO(2) via similar general pathways, Rhodococcus depends to a much higher extent on carboxylations reactions with external CO(2) owing to the formation of odd-numbered fatty acids. As a general consequence, heterotrophic fixation of CO(2) should be taken into account in investigations of degradation experiments using isotope tracer compounds.

Quantifying microbial utilization of petroleum hydrocarbons in salt marsh sediments by using the 13C content of bacterial rRNA

Natural remediation of oil spills is catalyzed by complex microbial consortia. Here we took a whole-community approach to investigate bacterial incorporation of petroleum hydrocarbons from a simulated oil spill. We utilized the natural difference in carbon isotopic abundance between a salt marsh ecosystem supported by the 13C-enriched C4 grass Spartina alterniflora and 13C-depleted petroleum to monitor changes in the 13C content of biomass. Magnetic bead capture methods for selective recovery of bacterial RNA were used to monitor the 13C content of bacterial biomass during a 2-week experiment. The data show that by the end of the experiment, up to 26% of bacterial biomass was derived from consumption of the freshly spilled oil. The results contrast with the inertness of a nearby relict spill, which occurred in 1969 in West Falmouth, MA. Sequences of 16S rRNA genes from our experimental samples also were consistent with previous reports suggesting the importance of Gamma- and Deltaproteobacteria and Firmicutes in the remineralization of hydrocarbons. The magnetic bead capture approach makes it possible to quantify uptake of petroleum hydrocarbons by microbes in situ. Although employed here at the domain level, RNA capture procedures can be highly specific. The same strategy could be used with genus-level specificity, something which is not currently possible using the 13C content of biomarker lipids.

Tracing 2,4-D metabolism in Cupriavidus necator JMP134 with 13C-labelling technique and fatty acid profiling

The use of stable isotope probing of fatty acid methyl esters (FAME-SIP) is a powerful tool to study the microorganisms involved in xenobiotic biodegradation in soil. Nevertheless, it is important to determine how representative these molecules are of microorganisms both qualitatively and quantitatively. Using Cupriavidus necator JMP134 as a simple experimental model, we showed that the (13)C-labelling technique can be used both at a global (here defined as cellular, medium and CO(2)) and molecular level to study the metabolism of 2,4-Dichlorophenoxyacetic acid (2,4-D). Although isotopic fractionation among substrate, biomass and FAME were observed, this technique could be used when using a highly (13)C-labelled substrate. Global (13)C analyses gave similar results to those obtained with traditional (14)C-labelling methods. After 10 days of incubation 59% of ring-C was mineralized and about 30% remained in the liquid medium. A maximum of 11% was incorporated into the biomass after 3 days. The assimilation yield of chain-C into the biomass was about half that of ring-C, suggesting a preferential use of chain-C for energy acquisition. Molecular analysis of the lipid fraction evidenced that the incorporation of the labelled 2,4-D did not correspond to a bioaccumulation of pesticide residues but to the metabolism of the 2,4-D carbons for FAME synthesis. Provided the labelling is located on the benzenic ring, the assessment of (13)C-FAME is a robust method to quantify the incorporation of (13)C into the whole microbial biomass. However, the variability of the (13)C incorporation among FAME due to physiological processes has to be considered in complex biological systems. The coupling of bulk and molecular studies with a simple model as C. necator JMP134 is a good approach for testing FAME-SIP.

Carbon-isotopic analysis of microbial cells sorted by flow cytometry

One of the outstanding current problems in both geobiology and environmental microbiology is the quantitative analysis of in situ microbial metabolic activities. Techniques capable of such analysis would have wide application, from quantifying natural rates of biogeochemical cycling to identifying the metabolic activity of uncultured organisms. We describe here a method that represents one step towards that goal, namely the high-precision measurement of ¹³ C in specific populations of microbial cells that are purified by fluorescence-activated cell sorting (FACS). Sorted cells are concentrated on a Teflon membrane filter, and their ¹³ C content is measured by coupling an isotope ratio mass spectrometer (IRMS) with a home-built spooling wire microcombustion (SWiM) apparatus. The combined instrumentation provides measurements of δ¹³ C in whole cells with precision better than 0.2‰ for samples containing as little as 25 ng of carbon. When losses associated with sample handling are taken into account, isotopic analyses require sorting roughly 10⁴ eukaryotic or 10⁷ bacterial cells per sample. Coupled with ¹³ C-labelled substrate additions, this approach has the potential to directly quantify uptake of metabolites in specific populations of sorted cells. The high precision afforded by SWiM-IRMS also permits useful studies of natural abundance variations in ¹³ C. The approach is equally applicable to specific populations of cells sorted from multicellular organisms.

Use of field-based stable isotope probing to identify adapted populations and track carbon flow through a phenol-degrading soil microbial community

The goal of this field study was to provide insight into three distinct populations of microorganisms involved in in situ metabolism of phenol. Our approach measured 13CO2 respired from [13C]phenol and stable isotope probing (SIP) of soil DNA at an agricultural field site. Traditionally, SIP-based investigations have been subject to the uncertainties posed by carbon cross-feeding. By altering our field-based, substrate-dosing methodologies, experiments were designed to look beyond primary degraders to detect trophically related populations in the food chain. Using gas chromatography-mass spectrometry (GC/MS), it was shown that (13)C-labeled biomass, derived from primary phenol degraders in soil, was a suitable growth substrate for other members of the soil microbial community. Next, three dosing regimes were designed to examine active members of the microbial community involved in phenol metabolism in situ: (i) 1 dose of [13C]phenol, (ii) 11 daily doses of unlabeled phenol followed by 1 dose of [13C]phenol, and (iii) 12 daily doses of [13C]phenol. GC/MS analysis demonstrated that prior exposure to phenol boosted 13CO2 evolution by a factor of 10. Furthermore, imaging of 13C-treated soil using secondary ion mass spectrometry (SIMS) verified that individual bacteria incorporated 13C into their biomass. PCR amplification and 16S rRNA gene sequencing of 13C-labeled soil DNA from the 3 dosing regimes revealed three distinct clone libraries: (i) unenriched, primary phenol degraders were most diverse, consisting of alpha-, beta-, and gamma-proteobacteria and high-G+C-content gram-positive bacteria, (ii) enriched primary phenol degraders were dominated by members of the genera Kocuria and Staphylococcus, and (iii) trophically related (carbon cross-feeders) were dominated by members of the genus Pseudomonas. These data show that SIP has the potential to document population shifts caused by substrate preexposure and to follow the flow of carbon through terrestrial microbial food chains.

Moving-Wire Device for Carbon Isotopic Analyses of Nanogram Quantities of Nonvolatile Organic Carbon

We describe a moving-wire analyzer for measuring 13C in dissolved, involatile organic materials. Liquid samples are first deposited and dried on a continuously spooling nickel wire. The residual sample is then combusted as the wire moves through a furnace, and the evolved CO2 is analyzed by continuous-flow isotope ratio mass spectrometry. A typical analysis requires 1 microL of sample solution and produces a CO2 peak approximately 5 s wide. The system can measure "bulk" delta13C values of approximately 10 nmol of organic carbon with precision better than 0.2 per thousand. For samples containing approximately 1 nmol of C, precision is approximately 1 per thousand. Precision and sensitivity are limited mainly by background noise derived from carbon within the wire. Instrument conditions minimizing that background are discussed in detail. Accuracy is better than 0.5 per thousand for nearly all dissolved analytes tested, including lipids, proteins, nucleic acids, sugars, halocarbons, and hydrocarbons. The sensitivity demonstrated here for 13C measurements represents a approximately 1000-fold improvement relative to existing elemental analyzers and should allow the use of many new preparative techniques for collecting and purifying nonvolatile biochemicals for isotopic analysis.

Influence of the growth substrate on ester-linked phospho- and glycolipid fatty acids of PAH-degrading Mycobacterium sp. LB501T

The influences of poorly water-soluble anthracene on ester-linked phospholipid fatty acid (PLFA) and glycolipid fatty acid (GLFA) profiles of Mycobacterium sp. LB501T were studied. Bacteria were cultivated on either anthracene or glucose (one culture with successively amended small doses of this substrate and one with excess concentrations) to distinguish between influences of the chemical structure and the bioavailability of the growth substrate. Results revealed that GLFA and PLFA profiles of M. sp. LB501T depended on the availability and the structure of the carbon source. Fatty acid profiles obtained with anthracene differed from those obtained with excess glucose. They were interpreted as a specific adaptation to this poorly bioavailable polycyclic aromatic hydrocarbon (PAH). In contrast, profiles obtained with low glucose concentrations showed clear signs of starvation stress. Stable carbon isotopic ratios (delta13C) of GLFA and PLFA of M. sp. LB501T were analysed to characterize the 13C-fractionation during the biosynthesis of individual fatty acids and to evaluate their value as markers for substrate usage. Although the delta13C values of PLFA and GLFA showed differential isotope fractionation during anthracene- and glucose-degradation, they were sufficiently distinct to be used as signatures of bacterial substrate usage.

Isolation of small-subunit rRNA for stable isotopic characterization

Small-subunit ribosomal RNA (SSU rRNA) has several characteristics making it a good candidate biomarker compound: it is found in bacteria, archaea and eukaryotes; it is quickly degraded extracellularly, hence SSU rRNA extracted from a sample probably derives from the currently active population; it includes both conserved and variable regions, allowing the design of capture probes at various levels of phylogenetic discrimination; and rRNA sequences from uncultured species can be classified by comparison with the large and growing public database. Here we present a method for isolation of specific classes of rRNAs from mixtures of total RNA, employing biotin-labelled oligonucleotide probes and streptavidin-coated paramagnetic beads. We also show that the stable carbon isotope composition of Escherichia coli total RNA and SSU rRNA reflects that of the growth substrate for cells grown on LB, M9 glucose and M9 acetate media. SSU rRNA is therefore a promising biomarker for following the flow of carbon, and potentially nitrogen, in natural microbial populations. Some possible applications are discussed.

Carbon isotopic fractionations associated with thermophilic bacteria Thermotoga maritima and Persephonella marina

Stable carbon isotopes can provide insight into carbon cycling pathways in natural environments. We examined carbon isotope fractionations associated with a hyperthermophilic fermentative bacterium, Thermotoga maritima, and a thermophilic chemolithoautotrophic bacterium Persephonella marina. In T. maritima, phospholipid fatty acids (PLFA) are slightly enriched in 13C relative to biomass (epsilon = 0.1-0.8 per thousand). However, PLFA and biomass are depleted in 13C relative to the substrate glucose by approximately 8 per thousand. In P. marina, PLFA are 1.8-14.5 per thousand enriched in 13C relative to biomass, which suggests that the reversed tricarboxylic acid (TCA) cycle or the 3-hydroxypropionate pathway may be used for CO2 fixation. This is supported by small fractionation between biomass and CO2 (epsilon = -3.8 per thousand to -5.0 per thousand), which is similar to fractionations reported for other organisms using similar CO2 fixation pathways. Identification of the exact pathway will require biochemical assay for specific enzymes associated with the reversed TCA cycle or the 3-hydroxypropionate pathway.

Combination of biomolecular and stable isotope techniques to determine the origin of organic matter used by bacterial communities: application to sediment

Natural isotopic composition is a good tool to trace organic matter in ecosystems. Recent studies used a combination of molecular and stable isotope techniques to determine the origin of the organic carbon used by bacteria in the water column. In our study, we show that this procedure can be used for analysis of sediment bacterial communities with few modifications. In the water column, bacterial recovery is done before DNA extraction. In the sediment, we tested qualitatively and quantitatively a direct and indirect extraction of DNA. The direct extraction was the most efficient. It recovered between 3.1 and 15.8 microg DNA g(-1) dry sediment and the contamination of field samples by eucaryotic DNA was less than 13%. In this preliminary study of the salt marsh ecosystem, the delta(13)C values of DNA (-26 to - 24%) recovered from the sediment were close to the delta(13)C values of halophytic plants (-26.4 and - 25.3%) showing a relationship between plants and microorganisms. Thus, this procedure can be used to trace the flow of carbon through the sediment microbial biomass and to understand the variation of bacterial activity according to the inputs of allocthonous and autochtonous organic matter.

Ratios of carbon isotopes in microbial lipids as an indicator of substrate usage

The occurrence and abundance of microbial fatty acids have been used for the identification of microorganisms in microbial communities. However, these fatty acids can also be used as indicators of substrate usage. For this, a systematic investigation of the discrimination of the stable carbon isotopes by different microorganisms is necessary. We grew 11 strains representing major bacterial and fungal species with four different isotopically defined carbon sources and determined the isotope ratios of fatty acids of different lipid fractions. A comparison of the differences of delta13C values of palmitic acid (C16:0) with the delta13C values of the substrates revealed that the isotope ratio is independent of the growth stage and that most microorganisms showed enrichment of C16:0 with 13C when growing on glycerol. With the exception of Burkholderia gladioli, all microorganism showed depletion of 13C in C16:0 while incorporating the carbons of glucose, and most of them were enriched with 13C from mannose, with the exception of Pseudomonas fluorescens and the Zygomycotina. Usually, the glycolipid fractions are depleted in 13C compared to the phospholipid fractions. The delta13C pattern was not uniform within the different fatty acids of a given microbial species. Generally, tetradecanoic acid (C14:0) was depleted of 13C compared to palmitic acid (C16:0) while octadecanoic acid (C18:0) was enriched. These results are important for the calibration of a new method in which delta13C values of fatty acids from the environment delineate the use of bacterial substrates in an ecosystem.

Direct determination of carbon and nitrogen contents of natural bacterial assemblages in marine environments

In order to better estimate bacterial biomass in marine environments, we developed a novel technique for direct measurement of carbon and nitrogen contents of natural bacterial assemblages. Bacterial cells were separated from phytoplankton and detritus with glass fiber and membrane filters (pore size, 0.8 &mgr;m) and then concentrated by tangential flow filtration. The concentrate was used for the determination of amounts of organic carbon and nitrogen by a high-temperature catalytic oxidation method, and after it was stained with 4',6-diamidino-2-phenylindole, cell abundance was determined by epifluorescence microscopy. We found that the average contents of carbon and nitrogen for oceanic bacterial assemblages were 12.4 +/- 6.3 and 2.1 +/- 1.1 fg cell-1 (mean +/- standard deviation; n = 6), respectively. Corresponding values for coastal bacterial assemblages were 30.2 +/- 12.3 fg of C cell-1 and 5.8 +/- 1.5 fg of N cell-1 (n = 5), significantly higher than those for oceanic bacteria (two-tailed Student's t test; P < 0.03). There was no significant difference (P > 0.2) in the bacterial C:N ratio (atom atom-1) between oceanic (6.8 +/- 1.2) and coastal (5.9 +/- 1.1) assemblages. Our estimates support the previous proposition that bacteria contribute substantially to total biomass in marine environments, but they also suggest that the use of a single conversion factor for diverse marine environments can lead to large errors in assessing the role of bacteria in food webs and biogeochemical cycles. The use of a factor, 20 fg of C cell-1, which has been widely adopted in recent studies may result in the overestimation (by as much as 330%) of bacterial biomass in open oceans and in the underestimation (by as much as 40%) of bacterial biomass in coastal environments.

Stable-Isotope Analysis of a Combined Nitrification-Denitrification Sustained by Thermophilic Methanotrophs under Low-Oxygen Conditions

To simulate growth conditions experienced by microbiota at O(inf2)-limited interfaces of organic matter in compost, an experimental system capable of maintaining dual limitations of oxygen and carbon for extended periods, i.e., a pO(inf2)-auxostat, has been used. (sup15)N tracer studies on thermophilic (53(deg)C) decomposition processes occurring in manure-straw aggregates showed the emission of dinitrogen gas from the reactor as a result of simultaneous nitrification and denitrification at low pO(inf2) values (0.1 to 2.0%, vol/vol). The N loss was confirmed by nitrogen budget studies of the system. Depending on the imposed pO(inf2), 0.6 to 1.4 mmol of N/day (i.e., 20 to 40% of input N) was emitted as N(inf2). When the pO(inf2) was raised, the rates of both nitrification and denitrification increased instantaneously, indicating that ammonia oxidation was limited by oxygen. In auxostats permanently running at pO(inf2) >= 2% (vol/vol), the free ammonium pool was almost completely oxidized and was converted to nitrite plus nitrate and N(inf2) gas. Labelling of the auxostat with [(sup13)C]carbonate was conducted to reveal whether nitrification was of autotrophic or heterotrophic origin. Incorporation of (sup13)CO(inf2) into population-specific cellular compounds was evaluated by profiling the saponifiable phospholipid fatty acids (FAs) by using capillary gas chromatography and subsequently analyzing the (sup13)C/(sup12)C ratios of the individual FAs, after their combustion to CO(inf2), by isotope ratio mass spectrometry. Apart from the observed label incorporation into FAs originating from a microflora belonging to the genus Methylococcus (type X group), supporting nitrification of a methylotrophic nature, this analysis also corroborated the absence of truly autotrophic nitrifying populations. Nevertheless, the extent to which ammonia oxidation continued to exist in this thermophilic community suggested that a major energy gain could be associated with it.

Microbial utilization of estuarine dissolved organic carbon: a stable isotope tracer approach tested by mass balance

The natural stable isotope values of different plants have been used to trace the fate of organic carbon that enters estuarine ecosystems. Experiments were designed to determine the magnitude of (delta) (sup13)C changes of dissolved organic carbon (DOC) derived from tidal marsh vegetation that occurred during bacterial decomposition. Bacteria were grown on DOC leached from estuarine Spartina alterniflora and Typhus angustifolia plants. In four experiments, 25 to 80% of the initial carbon (2.6 to 9.1 mM organic C) was converted to bacterial biomass and CO(inf2). Mass balance calculations showed good recovery of total C and (sup13)C at the end of these experiments (100% (plusmn) 14% total C; (plusmn) 1(permil) (delta) (sup13)C). The (delta) (sup13)C values of DOC, bacterial biomass, and respired CO(inf2) changed only slightly in the four experiments by average values of -0.6, +1.4, and +0.5(permil), respectively. These changes are small relative to the range of (delta) (sup13)C values represented by different organic carbon sources to estuaries. Thus, microbial (delta) (sup13)C values determined in the field helped to identify the source of the carbon assimilated by bacteria.

Fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes to identify small phytoplankton by flow cytometry

Because of their tiny size (0.2 to 2 microns), oceanic picophytoplanktonic cells (either cultured strains or natural communities) are difficult to identify, and some basic questions concerning their taxonomy, physiology, and ecology are still largely unanswered. The present study was designed to test the suitability of in situ hybridization with rRNA fluorescent probes detected by flow cytometry for the identification of small photosynthetic eukaryotes. Oligonucleotide probes targeted against regions of the 18S rRNAs of Chlorophyta lineage (CHLO probe) and of non-Chlorophyta (NCHLO probe) algal species were designed. The CHLO and NCHLO probes, which differed by a single nucleotide, allowed discrimination of chlorophyte from nonchlorophyte cultured strains. The sensitivity of each probe was dependent upon the size of the cells and upon their growth stage. The mean fluorescence was 8 to 80 times higher for specifically labeled than for nonspecifically labeled cells in exponential growth phase, but it decreased sharply in stationary phase. Such taxon-specific probes should increase the applicability of flow cytometry for the rapid identification of cultured pico- and nanoplanktonic strains, especially those that lack taxonomically useful morphological features.

Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment

This study reports improvements in two of the key steps, lysis of indigenous cells and DNA purification, required for achieving a rapid nonselective protocol for extracting nucleic acids directly from sodium dodecyl sulfate (SDS)-treated sediment rich in organic matter. Incorporation of bead-mill homogenization into the DNA extraction procedure doubled the densitometrically determined DNA yield (11.8 micrograms of DNA.g [dry weight] of sediment-1) relative to incorporation of three cycles of freezing and thawing (5.2 micrograms of DNA.g [dry weight] of sediment-1). The improved DNA extraction efficiency was attributed to increased cell lysis, measured by viable counts of sediment microorganisms which showed that 2 and 8%, respectively, survived the bead-mill homogenization and freeze-thaw procedures. Corresponding measurements of suspensions of viable Bacillus endospores demonstrated that 2 and 94% of the initial number survived. Conventional, laser scanning epifluorescence phase-contrast, and differential interference-contrast microscopy revealed that small coccoid bacterial cells (1.2 to 0.3 micron long) were left intact after combined SDS and bead-mill homogenization of sediment samples. Estimates of the residual fraction of the fluorescently stained cell numbers indicated that 6% (2.2 x 10(8) cells.g [dry weight] of sediment-1) of the original population (3.8 x 10(9) cells.g [dry weight] of sediment-1) remained after treatment with SDS and bead-mill homogenization. Thus, lysis of total cells was less efficient than that of cells which could be cultured. The extracted DNA was used to successfully amplify nahR, the regulatory gene for naphthalene catabolism in Pseudomonas putida G7, by PCR.(ABSTRACT TRUNCATED AT 250 WORDS)

Isotopic biogeochemistry of the Oxford Clay Formation (Jurassic), UK

A total of 165 samples was obtained from the Oxford Clay Formation at seven different sites. Nearly all were from the Peterborough Member (Lower Oxford Clay), but seven were from the Stewartby and Weymouth Members (Middle and Upper Oxford Clay respectively). Five samples from the underlying Kellaways Formation were also examined. Stratigraphic relationships were estimated on the basis of ammonite subzones and results from all locations can be placed along a single stratigraphic scale. The following were determined for all samples: abundance and isotopic composition of organic carbon, abundances of carbonate carbon and total sulphur, and the Rock-Eval pyrolysis parameters hydrogen index, oxygen index and Tmax. For a subset of eight samples selected to be representative of geochemical and apparent palaeoenvironmental variations, soluble organic compounds were extracted and the isotopic composition of pristane, phytane, and long-chain n-alkanes determined by isotope-ratio-monitoring gas chromatograph mass spectrometry. Concentrations of organic carbon in samples from the Peterborough Member ranged from 0.5 to 16.6 % and delta values of total organic carbon (TOC) ranged from -27.7 to -23.1% v. PDB. Shales dominated by epifaunal bivalve assemblages have high concentrations of TOC and values of H index approaching 800, indicating preservation of hydrogen-rich organic material. Conversely, shell beds and calcareous and silty clay beds have lower abundances of TOC and values of H index dropping below 100, indicating extensive oxidation of the organic matter. Isotopic composition of pristane and phytane in the Peterborough and Stewartby Members average -31.7%, those in the Weymouth Member average -29.8. Values of delta for long-chain n-alkanes average -28%. Together these results indicate delta values for primary inputs as follows: terrestrial vascular plants, -23.5%; Peterborough Member algae, -28.2; Stewartby Member algae, -29.1%; Weymouth Member algae, -26.6% Comparison of primary delta values to those of TOC indicates that in some cases secondary processes enriched TOC relative to primary inputs by as much as 4%. Paleontological evidence in these same beds indicates development of extensive food-webs and supports attribution of this isotopic enrichment to heterotrophic reworking.